Vaxcyte Investor Presentation November 2021

Corporate Presentation

November 10, 2021

Forward-Looking Statements

This presentation contains forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. These statements include but are not limited to, statements related to the benefits of Vaxcyte's vaccine candidates; the process and timing of anticipated future development of Vaxcyte's vaccine candidates, including the timing and submission of an IND application for VAX-24 and the initiation of the VAX-24 Phase 1/2 clinical proof-of-concept study thereafter; the timing and availability of topline data for VAX-24; the ability to complete the manufacturing of the GMP drug product; the successful testing and release of the final drug product for VAX-24 and documentation of stability; the achievement of future funding milestones; the use and availability of funds from CARB-X; the nomination of a final vaccine candidate for VAX-PG; the market opportunity for our vaccines; our expectations regarding the potential benefits, spectrum coverage and immunogenicity of our vaccine candidates; the timing of the initiation, progress and expected results of our preclinical studies, clinical trials and research and development plans; and other statements that are not historical fact. The words "anticipate," "believe," "continue," "could," "designed," "estimate," "expect," "intend," "may," "plan," "potential," "predict," "project," "should," "target," "will," "would" and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.

These forward-looking statements are based on Vaxcyte's current expectations and actual results and timing of events could differ materially from those anticipated in such forward-looking statements as a result of risks and uncertainties, including, without limitation, risks related to Vaxcyte's product development programs, including development timelines, success and timing of chemistry, manufacturing and controls and related manufacturing activities; Vaxcyte's reliance on third-party manufacturers; potential delays or inability to obtain and maintain required regulatory approvals for its vaccine candidates; the risks and uncertainties inherent with preclinical and clinical development processes; the success, cost and timing of all development activities and clinical trials; sufficiency of cash and other funding to support Vaxcyte's development programs and other operating expenses; and the ongoing COVID-19 pandemic, which could materially and adversely affect Vaxcyte's business and operations. These and other risks are described more fully in Vaxcyte's filings with the Securities and Exchange Commission (SEC), including its Quarterly Report on Form 10-Q filed with the SEC on November 10, 2021 or in other documents Vaxcyte subsequently files with or furnishes to the SEC. Vaxcyte undertakes no duty or obligation to update any forward-

2 looking statements contained in this release as a result of new information, future events or changes in its expectations.

Vaxcyte Mission Statement

Seeking to improve global health by developing

superior & novel vaccines designed to prevent or treat

some of the most common & deadly infectious

diseases worldwide.

3

Key Corporate Highlights

Next-Generation Vaccine Company - Led by Pneumococcal Conjugate Vaccine (PCV) Franchise

Large Market

Opportunity for PCV

Franchise

Cell-Free

Protein Synthesis

Platform

Disciplined	Robust	Aligned
Target	Development	Critical
Selection	Pipeline	Resources

• Scalable PCV platform enabling broader-spectrumPCVs: VAX-24& VAX-XP
• Lead candidate: VAX-24
• • 24-valentPCV with potential to replace SOC
  • Anticipated IND filing in Q1:22(1)
  • Anticipated Phase 1/2 data readout in late '22- early '23(1)

4 (1) Guidance provided as of November 10, 2021.

• Leverages site- specific conjugation
• Permits production of
  "tough-to-make" antigens
• Demonstrated speed, flexibility, and scalability

• Targets well-defined	• Platform unlocks large
>$7B market segment	market opportunities:
• Honors well-	- VAX-A1: Novel Group A
understood PCV MOA	Strep conjugate vaccine
• Leverages established	- VAX-PG: Novel
surrogate immune	periodontitis therapeutic
endpoints and clinical	vaccine
pathways

• Strategic alignment with Lonza (manufacturing)
• Seasoned management team, directors and advisors
• Cash, cash equivalents and investments of $318.3M at 9/30/21

Experienced Team, Board of Directors, and Scientific Advisors

Outstanding Track Record in Vaccines and Biopharma

Management Team

Board of Directors

Grant Pickering, MBA

Jim Wassil, MS, MBA

Andrew Guggenhime,

Carlos Paya, MD, PhD

Annie Drapeau

Halley Gilbert

CEO & Co-founder

COO

MBA

Chair

President & CFO

Peter Hirth, PhD

Michael Kamarck, PhD

Teri Loxam

Heath Lukatch, PhD

Kurt von Emster

Grant Pickering

Jeff Fairman, PhD	Paul Sauer, MBA	Harp Dhaliwal, MBA	Scientific Advisory Board
VP Research &	SVP PD & Manufacturing	SVP Commercial
Co-founder		Manufacturing & Supply
	Jeff Almond, PhD		Tony Ford-Hutchinson,		Emmanuel Hanon,
		Chain
						PhD		PhD

Bill Hausdorff, PhD	Tom Monath, MD	Emmanuel Walter,
		MD, MPH

5